Sat Oct 15 15:39:15 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:39:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3176 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5910283 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 0.3299999 49.17300 ymin,ymax (A): -7.856000 49.36700 zmin,zma (A): 0.6990000 60.93300 x,y,z range (A): 48.84300 57.22300 60.23400 scale (grids/A): 0.5910283 object centre (A): 24.75150 20.75550 30.81600 number of atom coordinates read : 3176 total number of charged atoms : 3005 net assigned charge : -9.9990666E-02 assigned positive charge : 475.2100 centred at (gu) : 89.52620 89.26031 90.94370 assigned negative charge : -475.3110 centred at (gu) : 89.43410 89.18089 90.89944 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7343 nv = 96 ne = 84 npr = 65408 no. pairs analyzed = 65408 no. exposed pairs = 3704 no. arc points = 25154 no. surface atoms = 1267 nbur = 1909 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 340 mr = 4283 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.3800000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2504 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2065960E-09 1.8438402E-09 midg,1,midg; midg,igrid,midg -3.2187430E-09 2.2232403E-09 1,midg,midg; igrid,midg,midg -3.5090526E-09 2.7391551E-09 gauss-seidel spectral radius is 0.9852299 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 15:39:18 rms-change max change #iterations 0.1135113 15.50441 at 10iterations 9.6960636E-03 1.395168 at 20iterations 1.0149806E-03 0.1487122 at 30iterations 2.2790499E-04 3.7891388E-02 at 40iterations 7.1105707E-05 1.2508869E-02 at 50iterations finished qdiffx linear iterations at : 15:39:27 total time elapsed so far: 5.110000 # loops : 50 mean,max change (kT/e) : 7.1105707E-05 1.2508869E-02 energy calculations done at 5.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.280000 DelPhi exited at 15:39:28 5.284u 0.468s 0:13.30 43.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:39:30 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3176 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.773085 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 0.3299999 49.17300 ymin,ymax (A): -7.856000 49.36700 zmin,zma (A): 0.6990000 60.93300 x,y,z range (A): 48.84300 57.22300 60.23400 scale (grids/A): 1.773085 object centre (A): 24.75150 20.75550 30.81600 number of atom coordinates read : 3176 total number of charged atoms : 3005 net assigned charge : -9.9990666E-02 assigned positive charge : 475.2100 centred at (gu) : 88.57780 87.78046 92.83020 assigned negative charge : -475.3110 centred at (gu) : 88.30191 87.54246 92.69801 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25154 grid for indexing accessible points = 1.400000 m= 29334 mr = 58253 m= 3868 mr = 22394 m= 140 mr = 2422 m= 0 mr = 40 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3091 time to turn everything in is 0.7100000 number of dielectric boundary points 31190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 23457 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5910283 object centre at (A) : 24.75150 20.75550 30.81600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4799900E-03 2.0342171E-03 midg,1,midg; midg,igrid,midg -1.6370654E-02 2.0261970E-03 1,midg,midg; igrid,midg,midg -9.8020136E-03 9.7560175E-03 gauss-seidel spectral radius is 0.9984831 estimated iterations to convergence 204 setup time was (sec) 1.070000 now iterating at: 15:39:35 rms-change max change #iterations 4.134038 155.7102 at 10iterations 1.862747 63.15506 at 20iterations 0.8423043 26.25149 at 30iterations 0.3790166 12.24317 at 40iterations 0.1716749 5.875097 at 50iterations 7.7312157E-02 2.526206 at 60iterations 3.5033695E-02 1.039860 at 70iterations 1.5879871E-02 0.5129433 at 80iterations 7.2827474E-03 0.2589960 at 90iterations 3.3891019E-03 0.1118393 at 100iterations 1.6548310E-03 5.3357124E-02 at 110iterations 8.6204137E-04 3.5354614E-02 at 120iterations finished qdiffx linear iterations at : 15:39:56 total time elapsed so far: 12.46000 # loops : 120 mean,max change (kT/e) : 8.6204137E-04 3.5354614E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 15:39:57 12.635u 0.542s 0:27.53 47.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:39:57 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3176 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.659627 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 0.3299999 49.17300 ymin,ymax (A): -7.856000 49.36700 zmin,zma (A): 0.6990000 60.93300 x,y,z range (A): 48.84300 57.22300 60.23400 scale (grids/A): 2.659627 object centre (A): 24.75150 20.75550 30.81600 number of atom coordinates read : 3176 total number of charged atoms : 3005 net assigned charge : -9.9990666E-02 assigned positive charge : 475.2100 centred at (gu) : 87.86654 86.67023 94.24511 assigned negative charge : -475.3110 centred at (gu) : 87.45280 86.31357 94.04688 start vw surface at 0.1300000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 187533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25154 grid for indexing accessible points = 1.400000 m= 97503 mr = 141021 m= 32926 mr = 81524 m= 6613 mr = 26930 m= 628 mr = 5022 m= 29 mr = 397 m= 0 mr = 15 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 10435 time to turn everything in is 1.750000 number of dielectric boundary points 70323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 24034 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.773085 object centre at (A) : 24.75150 20.75550 30.81600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3328089 -0.1097350 midg,1,midg; midg,igrid,midg -0.3558586 3.3588078E-02 1,midg,midg; igrid,midg,midg -0.1100630 0.1223946 gauss-seidel spectral radius is 0.9992232 estimated iterations to convergence 283 setup time was (sec) 2.170000 now iterating at: 15:40:02 rms-change max change #iterations 9.966863 269.8971 at 10iterations 5.729643 118.1973 at 20iterations 3.281972 66.23083 at 30iterations 1.868002 39.63764 at 40iterations 1.065526 19.28318 at 50iterations 0.6060517 11.22419 at 60iterations 0.3444368 6.915363 at 70iterations 0.1961370 3.820684 at 80iterations 0.1114680 1.865597 at 90iterations 6.3297115E-02 1.064360 at 100iterations 3.5972465E-02 0.6282234 at 110iterations 2.0424850E-02 0.3796601 at 120iterations 1.1693396E-02 0.2128220 at 130iterations 6.7272391E-03 0.1263924 at 140iterations 3.9141509E-03 6.9965363E-02 at 150iterations 2.3418826E-03 4.2566299E-02 at 160iterations 1.4564325E-03 3.0894279E-02 at 170iterations 9.5991453E-04 2.0004272E-02 at 180iterations finished qdiffx linear iterations at : 15:40:48 total time elapsed so far: 22.45000 # loops : 180 mean,max change (kT/e) : 9.5991453E-04 2.0004272E-02 energy calculations done at 22.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.61000 DelPhi exited at 15:40:50 22.618u 0.597s 0:53.09 43.6% 0+0k 0+0io 0pf+0w